{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T11:28:58Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 23.6, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a0955f-8a18-7c41-ab37-0b29acaca03b\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: mutation breeding\nSense to describe: (none recorded)\nDomain code: XCT.REL\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 044: 10", "usd": 0.0, "recall": true }, "codex": { "seconds": 77.0, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a0955f-8a12-7b01-bb37-7f2e7293f9cb\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: mutation breeding\nRegistry id: vr.tr.mutation-breeding\nPlane / domain: XCT / XCT.REL\nRegistry definition: (none recorded)\nNames folded into this entr" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:39:29+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:30+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q3330905", "registryId": "vr.tr.mutation-breeding", "name": "mutation breeding", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "XCT.REL" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q3330905/", "model": { "registry_id": "vr.tr.mutation-breeding", "name": "mutation breeding", "purpose": "Enable an agent to recognise mutation breeding, assess evidence that induced variation produces a useful heritable trait, and decide whether breeding material should advance, be retested, or be rejected.", "definition": "Mutation breeding is a plant-breeding approach that deliberately induces genetic mutations using physical or chemical mutagens and selects plants with useful, heritable traits for further breeding or cultivation.", "scope_statement": "This model owns the conceptual boundaries and evaluation logic of mutation breeding for vr.tr.mutation-breeding: deliberate mutation induction connected to selection and breeding improvement, provisionally centred on plants while retaining the registry placement XCT / XCT.REL.", "in_scope": [ "Definitions of mutation breeding and the evidence required to classify a breeding programme as an instance", "Relationships between starting germplasm, mutation induction, descendant populations and selected material", "Selection objectives, screening methods and evidence of useful variation", "Inheritance, segregation, chimerism and stability through the intended propagation route", "Decisions to retain, cross, retest, discard or advance mutant-derived material" ], "out_of_scope": [ "General plant breeding methods except where they incorporate induced mutant material", "Detailed operation of irradiation equipment or chemical mutagen treatment protocols", "Standalone descriptions of mutagen substances, radiation sources or DNA repair mechanisms", "Complete organism, accession or cultivar models", "Jurisdiction-specific release, marketing and intellectual property determinations", "Targeted genome editing as a separate technique, with its terminology boundary recorded here" ], "distinguishing_features": [ "A qualifying programme connects deliberately induced variation to a breeding objective and selection; exposure or mutagenesis alone is insufficient.", "Mutation induction contributes new variation, whereas crossing alone recombines variation already present in the parents.", "A spontaneous variant selected without deliberate induction is distinguished from an induced mutant, even when both enter similar breeding pipelines.", "Conventional mutation breeding does not specify the exact desired sequence change in advance; targeted editing requires an explicit boundary decision.", "A treatment-associated phenotype is a candidate observation until inheritance or persistence through the intended propagation route has been demonstrated." ], "characteristics": [ { "name": "Definition adopted", "kind": "category", "unit_or_values": "Induced-mutation breeding; broader mutation-based improvement; contested or unspecified usage", "why_it_matters": "Makes inclusion decisions attributable to a stated definition rather than the programme's label." }, { "name": "Starting material", "kind": "relation", "unit_or_values": "Links to species, accession or cultivar, genotype information and treated tissue", "why_it_matters": "Establishes the baseline against which variation and improvement are judged." }, { "name": "Mutation origin", "kind": "category", "unit_or_values": "Physical induction; chemical induction; combined induction; spontaneous; uncertain; other documented mechanism", "why_it_matters": "Separates programme membership from cases requiring exclusion or boundary review." }, { "name": "Treatment exposure record", "kind": "measurement", "unit_or_values": "Method-dependent quantities, such as absorbed dose in Gy or chemical concentration and exposure duration, with units and provenance", "why_it_matters": "Supports comparison of treated populations without treating unlike exposures as equivalent." }, { "name": "Propagation and generation", "kind": "state", "unit_or_values": "Sexual or vegetative route; generation or propagation-cycle designation with its local definition", "why_it_matters": "Determines how transmission and stability should be evaluated." }, { "name": "Selection response", "kind": "measurement", "unit_or_values": "Trait-specific effect relative to a named comparator, with uncertainty and test conditions", "why_it_matters": "Distinguishes useful improvement from novelty or measurement noise." }, { "name": "Screening yield", "kind": "measurement", "unit_or_values": "Retained candidates divided by screened units, with counts and the unit of independence stated", "why_it_matters": "Makes selection efficiency interpretable without counting related descendants as independent mutation events." }, { "name": "Transmission evidence", "kind": "state", "unit_or_values": "Untested; observed once; segregating; reproducible through specified propagation; unstable; unresolved", "why_it_matters": "Prevents a promising first observation from being treated as an established breeding resource." }, { "name": "Breeding disposition", "kind": "state", "unit_or_values": "Candidate; retest; retain; cross or backcross; advance; discard", "why_it_matters": "Connects evidence and unresolved limitations to an explicit next action." } ], "affordances": [ "Classify a reported programme against an explicit definition of mutation breeding.", "Trace selected material to starting germplasm, treatment and subsequent breeding steps.", "Compare candidate performance against parental and breeding-standard controls.", "Identify missing evidence for inheritance, clonal stability or mutation attribution.", "Recommend retesting, propagation, crossing, advancement or rejection against stated criteria." ], "agent_conduct": { "may": [ "Explain what mutation breeding is and how it differs from genetic modification and conventional crossing.", "Report which crop varieties are documented as products of mutation breeding, citing the registry." ], "must_not": [ "Provide instructions for operating radiation sources or handling chemical mutagens outside licensed facilities.", "Misstate the regulatory status of a mutation-bred variety in a given jurisdiction.", "Describe mutation-bred crops as untested or dangerous, or as identical to wild types, without evidence.", "Release untested breeding material into fields outside approved trials." ], "requires_human": [ "Releasing a new mutant line for field cultivation.", "Labelling decisions about mutation-bred produce for consumers." ] }, "ethics": { "considerations": [ "Mutagens and radiation sources put breeding staff at risk and must stay under licensed control.", "Farmers and consumers have a stake in honest information about how crops were bred." ], "affected_parties": [ "Breeding staff", "Farmers", "Consumers" ] }, "owners": { "steward": "The breeder or breeding institution; variety registration authorities record released varieties.", "master_systems": [ "National variety registers", "Mutant variety databases kept by international agencies" ] }, "visual_identification": [ "Mutation-bred plants look like ordinary crops; the breeding method is not visible in the field.", "Evidence of origin is found in variety registration and breeding records, not in the plant." ], "failure_modes_and_hazards": [ "Mishandled radiation sources or chemical mutagens can injure workers.", "Unintended mutations can carry undesired traits into a variety if selection is poor." ], "what_it_is_for": [ "Mutation breeding is used in crop improvement to create heritable variation from which breeders select useful plant traits.", "It is encountered in agricultural research and breeding programs seeking changes in qualities such as disease resistance, maturity or product composition.", "Selected plants require evaluation because induced mutations do not necessarily produce useful or stable outcomes." ], "standards_and_regulation": [ "Radiation Protection and Safety of Radiation Sources: International Basic Safety Standards, issued by the International Atomic Energy Agency and co-sponsoring organizations, applies to radiation protection in irradiation-based breeding work.", "The Globally Harmonized System of Classification and Labelling of Chemicals, published by the United Nations Economic Commission for Europe, provides the framework for communicating hazards of chemical mutagens." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q3330905: mutation breeding", "url": "https://www.wikidata.org/wiki/Q3330905", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Mutation breeding", "url": "https://en.wikipedia.org/wiki/Mutation_breeding", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "definition-and-boundaries", "name": "Definition and boundaries", "description": "Establish what makes a programme mutation breeding and which neighbouring techniques require separate treatment.", "rationale": "The registry supplies no definition, so the model must expose its interpretation and competing usages.", "layers": [ { "id": "induction-to-improvement", "name": "Induction to improvement", "description": "Connect variation generation to selection for a breeding purpose.", "findings": [ { "id": "qualifying-breeding-instance", "name": "Qualifying breeding instance", "description": "Use induced variation followed by selection and breeding use as the provisional core interpretation. The IAEA describes mutation induction as generating variation for mutant selection and plant breeding: [IAEA archival description](https://archives-catalogue.iaea.org/Search6/Details/archive/110206048).", "questions": [ { "text": "Which authority's definition is adopted, and does it require deliberate mutation induction?", "kind": "definition", "id": "qualifying-breeding-instance-q01" }, { "text": "What breeding objective and selection activity distinguish this instance from a mutagenesis experiment?", "kind": "boundary", "id": "qualifying-breeding-instance-q02" } ] } ] }, { "id": "neighbouring-techniques", "name": "Neighbouring techniques", "description": "Resolve overlap with spontaneous variation, tissue-culture variation and targeted editing.", "findings": [ { "id": "technique-inclusion-rules", "name": "Technique inclusion rules", "description": "Record inclusion rules explicitly, including whether the term describes mutation induction itself or a larger programme using mutant-derived parents.", "questions": [ { "text": "How does the adopted definition treat spontaneous sports, somaclonal variation and targeted genome editing?", "kind": "boundary", "id": "technique-inclusion-rules-q01" }, { "text": "When a mutant is used in later crosses, what evidence justifies describing the resulting programme or cultivar as mutation-derived?", "kind": "provenance", "id": "technique-inclusion-rules-q02" } ] } ] } ] }, { "id": "germplasm-and-induction-lineage", "name": "Germplasm and induction lineage", "description": "Establish what was treated and how candidate material descends from it.", "rationale": "A mutation claim cannot be evaluated without distinguishing starting variation, treatment history and subsequent ancestry.", "layers": [ { "id": "starting-genetic-background", "name": "Starting genetic background", "description": "Identify the biological baseline and relevant reproductive properties.", "findings": [ { "id": "baseline-material-identity", "name": "Baseline material identity", "description": "Record accession identity, starting heterogeneity, treated tissue and reproductive context before interpreting new variation.", "questions": [ { "text": "Which accession, cultivar and tissue supplied the treated material, and how was identity verified?", "kind": "provenance", "id": "baseline-material-identity-q01" }, { "text": "What baseline heterogeneity, ploidy and reproductive characteristics could affect detection or transmission of a variant?", "kind": "measurement", "id": "baseline-material-identity-q02" } ] } ] }, { "id": "treatment-and-descendant-links", "name": "Treatment and descendant links", "description": "Connect exposure records to independently traceable descendant families or clones.", "findings": [ { "id": "auditable-induction-history", "name": "Auditable induction history", "description": "Preserve the induction method, documented exposure, controls and ancestry without assuming every descendant difference was induced.", "questions": [ { "text": "Which treatment records and control materials support the claimed induction history?", "kind": "provenance", "id": "auditable-induction-history-q01" }, { "text": "How are independent treated units, descendant families, regenerated clones and later crosses distinguished?", "kind": "provenance", "id": "auditable-induction-history-q02" } ] } ] } ] }, { "id": "selection-and-trait-evidence", "name": "Selection and trait evidence", "description": "Make the desired improvement and the evidence used to select mutants explicit.", "rationale": "Mutation generation has breeding value only when candidates meet a defensible objective.", "layers": [ { "id": "breeding-targets", "name": "Breeding targets", "description": "Translate desired traits into measurable selection criteria.", "findings": [ { "id": "operational-selection-objective", "name": "Operational selection objective", "description": "Specify the desired trait change, relevant use environment and acceptable penalties in other traits.", "questions": [ { "text": "Which measurable trait change would count as useful improvement, relative to which parent or breeding standard?", "kind": "measurement", "id": "operational-selection-objective-q01" }, { "text": "Which fertility, yield, quality or other penalties would disqualify an otherwise promising candidate?", "kind": "action", "id": "operational-selection-objective-q02" } ] } ] }, { "id": "screening-reliability", "name": "Screening reliability", "description": "Evaluate whether screening identifies reproducible candidates rather than treatment injury or environmental responses.", "findings": [ { "id": "candidate-detection-and-confirmation", "name": "Candidate detection and confirmation", "description": "Separate initial screening hits from repeated phenotypic evidence and any molecular evidence supporting the trait.", "questions": [ { "text": "How many independent units were screened and retained, using which assay, controls and detection threshold?", "kind": "measurement", "id": "candidate-detection-and-confirmation-q01" }, { "text": "What repeat measurements distinguish the candidate trait from transient injury, environmental effects or assay error?", "kind": "measurement", "id": "candidate-detection-and-confirmation-q02" } ] } ] } ] }, { "id": "inheritance-and-propagation-stability", "name": "Inheritance and propagation stability", "description": "Evaluate retention of the selected trait through sexual or vegetative reproduction.", "rationale": "A variant must remain usable through the intended propagation route, and the relevant evidence differs between seeds and clones.", "layers": [ { "id": "sexual-transmission", "name": "Sexual transmission", "description": "Track generation structure, segregation and retention through crossing.", "findings": [ { "id": "generation-specific-inheritance", "name": "Generation-specific inheritance", "description": "Interpret candidate evidence using explicit generation definitions and observed transmission rather than assuming first-generation uniformity or fixation.", "questions": [ { "text": "What do the programme's generation labels mean, and in which generations was the trait observed?", "kind": "definition", "id": "generation-specific-inheritance-q01" }, { "text": "What progeny or crossing evidence supports inheritance, and what segregation or fertility limitations remain?", "kind": "measurement", "id": "generation-specific-inheritance-q02" } ] } ] }, { "id": "clonal-transmission", "name": "Clonal transmission", "description": "Assess tissue distribution of variation and retention through vegetative multiplication.", "findings": [ { "id": "chimerism-and-trait-retention", "name": "Chimerism and trait retention", "description": "Record whether the selected phenotype depends on a particular tissue lineage or propagation method. Chimera-free regeneration and retention of induced mutations are explicit research objectives for vegetatively propagated crops in this [FAO/IAEA project](https://www.iaea.org/newscenter/news/new-crp-development-of-integrated-techniques-for-induced-genetic-diversity-and-improvement-of-vegetatively-propagated-and-horticultural-tree-crops-d24014).", "questions": [ { "text": "What evidence establishes whether the candidate is genetically uniform or chimeric across relevant tissues?", "kind": "measurement", "id": "chimerism-and-trait-retention-q01" }, { "text": "Which propagation route and repeated cycles retain the desired phenotype, and what instability would trigger retesting?", "kind": "action", "id": "chimerism-and-trait-retention-q02" } ] } ] } ] }, { "id": "breeding-value-and-advancement", "name": "Breeding value and advancement", "description": "Judge candidate usefulness and select the next breeding step.", "rationale": "A confirmed variant can still lack practical value or require further breeding before advancement.", "layers": [ { "id": "comparative-performance", "name": "Comparative performance", "description": "Evaluate improvement across relevant conditions and distinguish performance evidence from causal attribution.", "findings": [ { "id": "validated-benefit-and-tradeoffs", "name": "Validated benefit and tradeoffs", "description": "Keep observed breeding benefit, environmental dependence and attribution to a particular mutation as separate judgments.", "questions": [ { "text": "How does the candidate perform against the original parent and an appropriate breeding standard across relevant environments?", "kind": "measurement", "id": "validated-benefit-and-tradeoffs-q01" }, { "text": "What evidence separates the selected mutation's contribution from background variation, linked changes or later crosses?", "kind": "provenance", "id": "validated-benefit-and-tradeoffs-q02" } ] } ] }, { "id": "candidate-disposition", "name": "Candidate disposition", "description": "Turn evidence into a documented breeding decision without equating advancement with cultivar release.", "findings": [ { "id": "evidence-based-next-step", "name": "Evidence-based next step", "description": "Record whether the material should be retained as a resource, crossed, retested, discarded or advanced, and identify evidence still required.", "questions": [ { "text": "Which unmet criteria determine whether to retest, cross or backcross, retain, discard or advance this material?", "kind": "action", "id": "evidence-based-next-step-q01" }, { "text": "Which linked cultivar-evaluation or release process must assess the material after this breeding decision?", "kind": "boundary", "id": "evidence-based-next-step-q02" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-confidence-notes", "name": "Check these first", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "The supplied domain code does not establish the intended sense; this account uses the established plant-breeding meaning.", "Terminology varies over whether selection of spontaneous mutants belongs under mutation breeding; this definition uses deliberate induced mutagenesis.", "Treatment doses, mutation frequencies and regulatory treatment require source checking for the particular crop, method and jurisdiction." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of mutation breeding this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-kinds", "name": "Kinds and varieties", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Radiation-induced mutation breeding", "Chemical mutagenesis-based breeding", "Mutation breeding using in vitro plant cultures" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of mutation breeding this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-real-world-use", "name": "Real-world use", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Developing crop varieties with improved disease resistance", "Changing plant height, architecture or maturity time", "Improving grain, fruit or seed quality", "Creating ornamental plants with novel flower colours or forms", "Introducing useful variation into breeding populations when existing variation is limited" ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of mutation breeding this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-measurements", "name": "Typical measurements", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "quantity": "Absorbed radiation dose", "typical_range": "Depends on radiation type, species, genotype and treated tissue; no universal working range", "unit": "gray (Gy)" }, { "quantity": "Mutant frequency", "typical_range": "Depends on the trait, treatment, generation and screening method", "unit": "mutants per screened population, often expressed as a percentage" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of mutation breeding this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-failure-modes-and-hazards", "name": "Failure modes and hazards", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Most induced mutations are neutral or harmful rather than useful, requiring extensive screening.", "Mutagen treatment can reduce germination, survival or fertility.", "Desirable mutants may carry additional harmful mutations that require further breeding to remove.", "Chimerism and environmental effects can make an apparent improvement fail to reproduce or transmit reliably.", "Ionizing radiation and chemical mutagens pose occupational hazards during treatment." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of mutation breeding this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-neighbours", "name": "Neighbouring kinds and how to tell them apart", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "name": "Conventional crossbreeding", "difference": "Crossbreeding recombines parental genetic variation through sexual reproduction; mutation breeding deliberately generates additional variation through mutagen treatment." }, { "name": "Genome editing", "difference": "Genome editing directs changes to selected genomic targets; conventional mutation breeding induces mutations without targeting a predetermined DNA sequence." }, { "name": "Transgenic breeding", "difference": "Transgenic breeding introduces genetic constructs; mutation breeding does not require introducing a transgene." }, { "name": "Somaclonal variation", "difference": "Somaclonal variation arises during tissue culture without necessarily applying a mutagen; mutation breeding can use cultured tissues but deliberately applies mutagenesis." }, { "name": "TILLING", "difference": "TILLING screens populations for mutations in specified genes; it can support mutation breeding but is a mutation-discovery method rather than the entire breeding process." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of mutation breeding this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the registry intend mutation breeding specifically in plants, or also analogous improvement programmes in microorganisms and other organisms?", "Which reference definitions should govern inclusion of spontaneous mutants, somaclonal variation and targeted mutagenesis?", "What crop- and propagation-specific evidence is sufficient to call a selected trait stable, particularly for useful chimeric forms?", "How much ancestry and causal evidence is required to classify a later cross-derived cultivar as a mutation-breeding outcome?", "Does XCT / XCT.REL intentionally classify this as a concept, or should the registry also link it to a breeding-method model in the activity plane?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 16, "questions": 26 } }